Ding, Yang. “Parametric RNA Partition Function Algorithms”, Boston College, 2010. http://hdl.handle.net/2345/1813.
In addition to the well-characterized messenger RNA, transfer RNA and ribosomal RNA, many new classes of noncoding RNA(ncRNA) have been discovered in the past few years. ncRNA has been shown to play important roles in multiple regulation and development processes. The increasing needs for RNA structural analysis software provide great opportunities on computational biologists. In this thesis I present three highly non-trivial RNA parametric structural analysis algorithms: 1) RNAhairpin and RNAmultiloop, which calculate parition functions with respect to hairpin number, multiloop number and multiloop order, 2) RNAshapeEval, which is based upon partition function calculation with respect to a fixed abstract shape, and 3) RNAprofileZ, which calculates the expected partition function and ensemble free energy given an RNA position weight matrix.I also describe the application of these software in biological problems, including evaluating purine riboswitch aptamer full alignment sequences to adopt their consensus shape, building hairpin and multiloop profiles for certain Rfam families, tRNA and pseudoknotted RNA secondary structure predictions. These algorithms hold the promise to be useful in a broad range of biological problems such as structural motifs search, ncRNA gene finders, canonical and pseudoknotted secondary structure predictions.